San Francisco Mayor Ed Lee announced a tentative agreement to launch a commuter shuttle pilot program requiring permits and fees for most companies operating employee buses in the city.

The corporate shuttles operated on behalf of tech giants like Apple, Facebook, Genentech and Google have become a sore spot locally amid complaints that they use public transit stops for free and delay buses operated by the San Francisco Municipal Transportation Agency. But for many, the private, tinted-window shuttles have also become a potent symbol of Silicon Valley elitism at a time when skyrocketing rents are forcing some residents to flee the city.

Housing and other activists have staged a series of protests against the shuttles in recent weeks, including one in Oakland last month during which a window was broken and tires were slashed.

Under the 18-month pilot program, a shuttle operator or employer will pay a daily fee based on the number of stops it makes. The average cost per company is expected to run about $100,000, adding up to approximately $1.5 million over the year-and-a-half program.

“This agreement will help the city realize the benefits that come with commuter shuttles, such as keeping thousands of cars off our roads and preventing gridlock, while ensuring companies pay their fair share and don’t delay our public transportation system,” Mayor Lee said in a statement.

The private shuttles eliminate some 45 million vehicle miles traveled per year, subtracting 761,000 metric tons of carbon emissions, according to city estimates.

The deal sets aside 200 bus stops, out of some 2,500 in the Muni system, as shared zones that participating companies can use. Private shuttle operators must abide by certain guidelines, including yielding to Muni buses.

The agreement does not apply to tour buses, airport shuttles, charter buses and similar operations.

The charges are only enough to recover agency costs. Under state law, SFMTA isn’t legally allowed to create fees that go beyond that, said Ed Reiskin, director of transportation for the agency.

Mayor Lee made the announcement during a press conference at MTA’s offices, alongside Reiskin and representatives from Genentech, Google and the Bay Area Council, a local business trade group.

“Google is really excited to begin working with you and the Bay Area Council and members of the community on our shared goal of efficient transportation around the Bay Area,” said Veronica Bell, senior manager of public policy and government relations at the search giant, during the event. “We see this pilot program as a good first step toward better integration and partnerships in the months ahead.”

The MTA’s board must still approve the agreement; it goes before the members on Jan. 21. Final approval is expected in late spring.